Globally installed software

Available as modules

• gcc/4.8.1
• python/2.7.6
• python/3.3.3
• R/3.0.2

Globally installed on all nodes

• Perl5.10
• pigz
• Python2.6
• BioPerl v1.61

Available as global SHARED modules

Modules can be found in:

 /cm/shared/modulefiles/SHARED/

• ALLPATHS-LG/48961
• augustus/2.7
• bedtools/2.18.0
• BLAST+/2.2.28
• blat/v35
• bowtie/2-2.2.1
• bwa/0.5.9
• bwa/0.7.5a
• cegma/2.4
• cufflinks/2.1.1
• exonerate/2.2.0-x86_64
• geneid/1.4.4
• genewise/2.2.3-rc7
• hmmer/3.1b1
• jellyfish/2.1.1
• MAFFT/7.130
• maker/2.28
• muscle/3.8.31
• Plink/1.07
• provean/1.1.3
• RepeatMasker/4.0.3
• RepeatModeler/1.0.7
• RAxML/8.0.0
• samtools/0.1.12a
• samtools/0.1.19
• snap/2013-11-29
• SOAPdenovo2/r240
• tophat/2.0.11

Adding a custom module directory to your environment

To allow the module program to find the custom module directory, the location of that directory has to be added to MODULEPATH variable.

export MODULEPATH=$MODULEPATH:/cm/shared/modulefiles/SHARED

This can be made permanent by adding this line of code to the .bash_profile file in the root of your home folder. To then load the modified MODULEPATH variable you have to load .bash_profile again:

source .bash_profile

This needs to be done only for terminals that are already open. Next time you login, .bash_profile will be loaded automatically.

You can check if the modules are found.

module avail

This should give output that includes something similar to this:

 --------------------------------------------------- /cm/shared/modulefiles/SHARED/ ---------------------------------------------------
 ALLPATHS-LG/48961      bwa/0.5.9              genewise/2.2.3-rc7     maker/2.28_mpi2        RepeatModeler/1.0.7
 augustus/2.7           bwa/0.7.5a             hmmer/3.1b1            muscle/3.8.31          samtools/0.1.12a
 bedtools/2.18.0        cegma/2.4              jellyfish/2.1.1        plink/1.07             samtools/0.1.19
 BLAST+/2.2.28          cufflinks/2.1.1        MAFFT/7.130            provean/1.1.3          snap/2013-11-29
 blat/v35               exonerate/2.2.0-x86_64 maker/2.28             RAxML/8.0.0            SOAPdenovo2/r240
 bowtie/2-2.2.1         geneid/1.4.4           maker/2.28_mpi         RepeatMasker/4.0.3     tophat/2.0.11

See also

• Using the B4F Cluster
• Installing domain specific software: installation by users
• Setting local variables
• Installing R packages locally
• Setting up and using a virtual environment for Python3
• modules specific for ABGC